4GL5

Structure of human placental aromatase complexed with designed inhibitor HDDG029 (compound 4)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Novel aromatase inhibitors by structure-guided design.

Ghosh, D., Lo, J., Morton, D., Valette, D., Xi, J., Griswold, J., Hubbell, S., Egbuta, C., Jiang, W., An, J., Davies, H.M.

(2012) J Med Chem 55: 8464-8476

  • DOI: 10.1021/jm300930n
  • Primary Citation of Related Structures:  
    3S7S, 3S79, 4GL5, 4GL7

  • PubMed Abstract: 

    • Human cytochrome P450 aromatase catalyzes with high specificity the synthesis of estrogens from androgens. Aromatase inhibitors (AIs) such as exemestane, 6-methylideneandrosta-1,4-diene-3,17-dione, are preeminent drugs for the treatment of estrogen-d ...

    Human cytochrome P450 aromatase catalyzes with high specificity the synthesis of estrogens from androgens. Aromatase inhibitors (AIs) such as exemestane, 6-methylideneandrosta-1,4-diene-3,17-dione, are preeminent drugs for the treatment of estrogen-dependent breast cancer. The crystal structure of human placental aromatase has shown an androgen-specific active site. By utilization of the structural data, novel C6-substituted androsta-1,4-diene-3,17-dione inhibitors have been designed. Several of the C6-substituted 2-alkynyloxy compounds inhibit purified placental aromatase with IC(50) values in the nanomolar range. Antiproliferation studies in a MCF-7 breast cancer cell line demonstrate that some of these compounds have EC(50) values better than 1 nM, exceeding that for exemestane. X-ray structures of aromatase complexes of two potent compounds reveal that, per their design, the novel side groups protrude into the opening to the access channel unoccupied in the enzyme-substrate/exemestane complexes. The observed structure-activity relationship is borne out by the X-ray data. Structure-guided design permits utilization of the aromatase-specific interactions for the development of next generation AIs.

    Organizational Affiliation: 

    Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA. ghoshd@upstate.edu



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 19A1A503Homo sapiensMutation(s): 0 
Gene Names: CYP19A1, ARO1, CYAR, CYP19
EC: 1.14.14.1 (PDB Primary Data), 1.14.14.14 (UniProt)
Find proteins for P11511 (Homo sapiens)
Explore P11511 
Go to UniProtKB:  P11511
NIH Common Fund Data Resources
PHAROS  P11511
GTEx  ENSG00000137869
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
G29
Query on G29
Download Ideal Coordinates CCD File 
A
(6alpha,8alpha)-6-(but-2-yn-1-yloxy)androsta-1,4-diene-3,17-dione
C23 H28 O3
GNDYBZKXORBCFO-KVAKACLVSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G29IC50:  112.30000305175781   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.329α = 90
b = 140.329β = 90
c = 118.733γ = 120
Software Package:
Software NamePurpose
HKL-3000data collection
CCP4model building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-08-13 
  • Released Date: 2012-09-12 
    • Deposition Author(s): Ghosh, D.

Revision History 

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2012-09-19
    Changes: Database references
  • Version 1.2: 2012-10-24
    Changes: Database references